From unknown Sun Aug 17 10:16:34 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#60729] [PATCH] gnu: Add cellsnp-lite. 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Wed, 11 Jan 2023 05:47:51 -0800 (PST) From: zimoun Date: Wed, 11 Jan 2023 14:47:44 +0100 Message-Id: <20230111134744.2551087-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32d; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32d.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) From: Simon Tournier * gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. --- gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..4ef9ec15b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li -;;; Copyright © 2021, 2022 Simon Tournier +;;; Copyright © 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2022 Navid Afkhami ;;; Copyright © 2022 Antero Mejr @@ -512,6 +512,48 @@ (define-public bedtools-2.18 (inputs (list samtools zlib)))) +(define-public cellsnp-lite + ;; Last release from November 2021 and does not contain fixes. + (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") + (revision "0")) + (package + (name "cellsnp-lite") + (version (git-version "1.2.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/single-cell-genetics/cellsnp-lite") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags #~(list (string-append "--with-htslib=" + #$(this-package-input "htslib"))))) + (inputs + (list curl + htslib + openssl + zlib)) + (native-inputs + (list autoconf)) + (home-page "https://cellsnp-lite.readthedocs.io") + (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data") + (description + "This package is designed to pileup the expressed alleles in +single-cell or bulk RNA-seq data, which can be directly used for donor +deconvolution in multiplexed single-cell RNA-seq data, particularly with other +packages, which assigns cells to donors and detects doublets as vireo, even +without genotyping reference. + +This package is the C version of the deprecated cellSNP implemented in Python. +Comparedto cellSNP, this package is more efficient with higher speed and less +memory usage.") + (license license:asl2.0)))) + (define-public pbcopper (package (name "pbcopper") base-commit: a8b2decf287498eeb51ef23712c5bd01b60cb18b -- 2.38.1 From unknown Sun Aug 17 10:16:34 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#60729: closed (Re: [bug#60729] [PATCH] gnu: Add cellsnp-lite.) Message-ID: References: <87edrzlc72.fsf@elephly.net> <20230111134744.2551087-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 60729 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 60729@debbugs.gnu.org Date: Thu, 12 Jan 2023 20:40:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1673556001-6400-1" This is a multi-part message in MIME format... ------------=_1673556001-6400-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #60729: [PATCH] gnu: Add cellsnp-lite. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 60729@debbugs.gnu.org. --=20 60729: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D60729 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1673556001-6400-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 60729-done) by debbugs.gnu.org; 12 Jan 2023 20:39:38 +0000 Received: from localhost ([127.0.0.1]:48677 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pG4MM-0001eH-5A for submit@debbugs.gnu.org; Thu, 12 Jan 2023 15:39:38 -0500 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21975) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pG4MK-0001e6-7z for 60729-done@debbugs.gnu.org; Thu, 12 Jan 2023 15:39:36 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1673555974; cv=none; d=zohomail.com; s=zohoarc; b=LkBo6SbwH5sQg6fOWkgR8Bu6vCf93KxRIdDEGNKFkXRPxEmh2Fs9EIwJ4FYEQG+T+WUJ/U8SykIQEt29pDlN8RwbmLKkE56KmmGQXVKH1eAXlQexXsLEJmoy3aiRmpl6S0oNIe9BXs2XM4t7a+d+2Uq80guiMpMd+0gnyK8yUZA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1673555974; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=v6GDijnANhv3Nb1fQbXfyLAGOT0tRjM4tIcy6NWNDSk=; b=JVTwUcViu3IAVOXyVQFlVkiBRUTFhqRJy7gZFlw12EcnmmujM2LFG3YZshUnRhPbTHCObMgL8mY+uvJv9vFn2gQHk3mmZyaalc/IphLbXbnd2TWof7J2eEnIYponyRaMDMlkPJDOtI2GpPJSlMvWqdaSOHBJtB1jjiG2eodExOI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1673555974; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=v6GDijnANhv3Nb1fQbXfyLAGOT0tRjM4tIcy6NWNDSk=; b=UEI4qSILVuqhsnU0EBjodTUcOeFRDZsKGwqBh/ZiZmyxsOVSpUOZp3e1svGcNkWP 6/FDz5Lk8He/KCBnoS9xuPqYPyK8sAHkTi02mCGOXvqqbDh91rZj9CFYhYceo37pu4V A28IDJP3iCjQF68tvNmgFmVUVfm0JFKfpXklN3Dc= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 1673555972650984.746140310471; Thu, 12 Jan 2023 12:39:32 -0800 (PST) References: <20230111134744.2551087-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#60729] [PATCH] gnu: Add cellsnp-lite. Date: Thu, 12 Jan 2023 21:38:59 +0100 In-reply-to: <20230111134744.2551087-1-zimon.toutoune@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87edrzlc72.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60729-done Cc: 60729-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) zimoun writes: > From: Simon Tournier > > * gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. Applied, thank you! -- Ricardo ------------=_1673556001-6400-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 11 Jan 2023 13:48:06 +0000 Received: from localhost ([127.0.0.1]:41968 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pFbSY-0001Xg-3A for submit@debbugs.gnu.org; Wed, 11 Jan 2023 08:48:06 -0500 Received: from lists.gnu.org ([209.51.188.17]:60892) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pFbSU-0001XD-AU for submit@debbugs.gnu.org; Wed, 11 Jan 2023 08:48:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pFbSO-0003qS-TG for guix-patches@gnu.org; Wed, 11 Jan 2023 08:48:00 -0500 Received: from mail-wm1-x32d.google.com ([2a00:1450:4864:20::32d]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pFbSN-0006CZ-4X for guix-patches@gnu.org; Wed, 11 Jan 2023 08:47:56 -0500 Received: by mail-wm1-x32d.google.com with SMTP id ay40so11135179wmb.2 for ; Wed, 11 Jan 2023 05:47:53 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=xjwkkFN/6RpTJ6Ervjp8dFQGYfItSlatilnv7W1wQZ8=; b=V+NptSd8RkR+x9TjfMcyBm6xMFIjiDtG6uFLWh1pvHARLQVEze+T9B452aj8npfEPb dm5jLpzbZGW0KwRobNzkmtysGH5rUTAgZMUc1OzSfNKrt4Cx5s0FF7tSxio8RB3gkA1t DFrStAkI500TT69v7C9uqBcP5nNPImtKAaTcIZj1KWTtlHV2JJrwPTABSwFlr/M/QuCs 0jK/GAe/B3wLGqK4eWizh/X8lD7dpJS59vQ0PUgjH8f1U9dgSJYOB4pbsZQarNYZ3xPi 2PK7fRgDSi+DapSC7V1KMTvIQU0zdDyyyeVn25xZeedW2T+HmK9/Rwi/1a+W3i3UEhyB 0qpw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=xjwkkFN/6RpTJ6Ervjp8dFQGYfItSlatilnv7W1wQZ8=; b=hyiEdn1c70i8fjJ4BQkp7ZzZvjzJMwZED/hblNRsClm4Se/5tm7UXnlWX/Po3Qigrp Vos5011JeBiG80MNKo5Ku9F/et4mpqgi5LwBCFjn2fRoKas4Z9Z6f/RuAtataj2XuUuT L9R3JNC+bsuScA//4ic7fEhJyTDPUaQRdFjhA+eJX5MzSPanF4G3leot06dWQGNZf7A2 BQdHXLDhnksmnHUNz0RAEtZuq6Tp9EoKy5Pq6CgHOrHlfaYAGfubg7XYm1EPv+H1dbEs kFowEdZWgI77RfQjz+4Ho+cyBMx+I688XWmWPNXGWHmeL/N1BbEvGEw8CDExl/tZ4UKh AOmw== X-Gm-Message-State: AFqh2koXkL4+dFE4UzZVJdA0dDYCyANjlDWUTjmUAk/WCGwrEbLeQUYM Fwl7/eYhd5ioJOp5PPXKbJqEG/Jtp9c= X-Google-Smtp-Source: AMrXdXut2OVxL+JrCWF6qkjUn8JADX+IHn51iLVWmzAe15r8FIzHcg9mrPvudxt/xX1/o6xRmJCZ2A== X-Received: by 2002:a05:600c:3ba0:b0:3d3:5a4a:9122 with SMTP id n32-20020a05600c3ba000b003d35a4a9122mr14355598wms.2.1673444871943; Wed, 11 Jan 2023 05:47:51 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id h10-20020a05600c2caa00b003cfd58409desm24078070wmc.13.2023.01.11.05.47.51 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 11 Jan 2023 05:47:51 -0800 (PST) From: zimoun To: guix-patches@gnu.org Subject: [PATCH] gnu: Add cellsnp-lite. Date: Wed, 11 Jan 2023 14:47:44 +0100 Message-Id: <20230111134744.2551087-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Debbugs-CC: rekado@elephly.net Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32d; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32d.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) From: Simon Tournier * gnu/packages/bioinformatics.scm (cellsnp-lite): New variable. --- gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..4ef9ec15b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21,7 +21,7 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li -;;; Copyright © 2021, 2022 Simon Tournier +;;; Copyright © 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2022 Navid Afkhami ;;; Copyright © 2022 Antero Mejr @@ -512,6 +512,48 @@ (define-public bedtools-2.18 (inputs (list samtools zlib)))) +(define-public cellsnp-lite + ;; Last release from November 2021 and does not contain fixes. + (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") + (revision "0")) + (package + (name "cellsnp-lite") + (version (git-version "1.2.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/single-cell-genetics/cellsnp-lite") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags #~(list (string-append "--with-htslib=" + #$(this-package-input "htslib"))))) + (inputs + (list curl + htslib + openssl + zlib)) + (native-inputs + (list autoconf)) + (home-page "https://cellsnp-lite.readthedocs.io") + (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data") + (description + "This package is designed to pileup the expressed alleles in +single-cell or bulk RNA-seq data, which can be directly used for donor +deconvolution in multiplexed single-cell RNA-seq data, particularly with other +packages, which assigns cells to donors and detects doublets as vireo, even +without genotyping reference. + +This package is the C version of the deprecated cellSNP implemented in Python. +Comparedto cellSNP, this package is more efficient with higher speed and less +memory usage.") + (license license:asl2.0)))) + (define-public pbcopper (package (name "pbcopper") base-commit: a8b2decf287498eeb51ef23712c5bd01b60cb18b -- 2.38.1 ------------=_1673556001-6400-1--